Im trying to impute some genotype data on the Michigan imputation server (https://imputationserver.sph.umich.edu/ ). For autosomes this works perfect and straightforward. However for chromosome X I ran into some trouble. Initially that Eagle v2.3 does not work on chromosome X and so you need to use shapeit. Then we I tried to impute chromosome X I get the error that there are heterozygous variants in my males...
Chromosome X check failed! java.io.IOException: Found haplotype 0/1 at pos 2703633 for male proband 1038_1 Found haplotype 0/1 at pos 2703633 for male proband 1700_1 Found haplotype 0/1 at pos 2703633 for male proband 2147_2 Found haplotype 0/1 at pos 2703633 for male proband 2296_3 Error during manifest file creation.
Then when I split males and females, I get the same error for males again and another error for females:
Chromosome X check failed! java.io.IOException: Something went wrong with the keepSamples male command Error during manifest file creation.
Then I started reading a bit about it and found that the PAR regions are there -> The non-PAR is located on chrX:2699520-154931043 on build hg19 (http://genome.sph.umich.edu/wiki/Minimac3_Cookbook_:_Chromosome_X_Imputation ), but all my 7495 chromosome X variants are in this area, so this does not help me much. Because I already tried splitting males and females did not work. Also because the variants here are in the PAR region, males can be heterozygous so just changing all the heterozygous variants of males to missing is not appropriate I think.
Does anyone has any recommendations for this? Or am I doing something completely wrong?